Starting phenix.real_space_refine on Sat Mar 7 10:03:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ukp_20808/03_2026/6ukp_20808.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ukp_20808/03_2026/6ukp_20808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ukp_20808/03_2026/6ukp_20808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ukp_20808/03_2026/6ukp_20808.map" model { file = "/net/cci-nas-00/data/ceres_data/6ukp_20808/03_2026/6ukp_20808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ukp_20808/03_2026/6ukp_20808.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 84 5.16 5 C 13209 2.51 5 N 3647 2.21 5 O 3759 1.98 5 H 20433 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41132 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5876 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5876 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5876 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5876 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5876 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5876 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5876 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 7.13, per 1000 atoms: 0.17 Number of scatterers: 41132 At special positions: 0 Unit cell: (158.24, 156.52, 118.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 O 3759 8.00 N 3647 7.00 C 13209 6.00 H 20433 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.11 Conformation dependent library (CDL) restraints added in 1.2 seconds 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4802 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 21 sheets defined 44.5% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 3.837A pdb=" N ARG A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 70 removed outlier: 3.967A pdb=" N LEU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 70 " --> pdb=" O TRP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.617A pdb=" N GLY A 89 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 90 " --> pdb=" O GLU A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 90' Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.282A pdb=" N PHE A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.835A pdb=" N ASN A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.664A pdb=" N ILE A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 217' Processing helix chain 'A' and resid 235 through 247 removed outlier: 3.515A pdb=" N LEU A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.524A pdb=" N VAL A 272 " --> pdb=" O HIS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.929A pdb=" N ARG A 336 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 369 removed outlier: 3.768A pdb=" N LEU A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.650A pdb=" N PHE B 43 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR B 47 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 70 removed outlier: 3.967A pdb=" N LEU B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS B 70 " --> pdb=" O TRP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.617A pdb=" N GLY B 89 " --> pdb=" O HIS B 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 90 " --> pdb=" O GLU B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 90' Processing helix chain 'B' and resid 144 through 160 removed outlier: 4.283A pdb=" N PHE B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 157 " --> pdb=" O GLU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.835A pdb=" N ASN B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.665A pdb=" N ILE B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 217' Processing helix chain 'B' and resid 235 through 247 removed outlier: 3.513A pdb=" N LEU B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 272 removed outlier: 3.524A pdb=" N VAL B 272 " --> pdb=" O HIS B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.928A pdb=" N ARG B 336 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 369 removed outlier: 3.768A pdb=" N LEU B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 369 " --> pdb=" O PHE B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 414 through 417 Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.650A pdb=" N PHE C 43 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS C 46 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR C 47 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 removed outlier: 3.967A pdb=" N LEU C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS C 70 " --> pdb=" O TRP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.616A pdb=" N GLY C 89 " --> pdb=" O HIS C 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 90 " --> pdb=" O GLU C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 86 through 90' Processing helix chain 'C' and resid 144 through 160 removed outlier: 4.283A pdb=" N PHE C 148 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN C 149 " --> pdb=" O LYS C 145 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 211 removed outlier: 3.835A pdb=" N ASN C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.665A pdb=" N ILE C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 217' Processing helix chain 'C' and resid 235 through 247 removed outlier: 3.514A pdb=" N LEU C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 272 removed outlier: 3.523A pdb=" N VAL C 272 " --> pdb=" O HIS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 333 through 337 removed outlier: 3.928A pdb=" N ARG C 336 " --> pdb=" O TYR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 369 removed outlier: 3.770A pdb=" N LEU C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C 362 " --> pdb=" O HIS C 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 369 " --> pdb=" O PHE C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 392 through 401 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 414 through 417 Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.650A pdb=" N PHE D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR D 47 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 70 removed outlier: 3.967A pdb=" N LEU D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS D 70 " --> pdb=" O TRP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.616A pdb=" N GLY D 89 " --> pdb=" O HIS D 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 90 " --> pdb=" O GLU D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 90' Processing helix chain 'D' and resid 144 through 160 removed outlier: 4.282A pdb=" N PHE D 148 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN D 149 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 157 " --> pdb=" O GLU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 211 removed outlier: 3.835A pdb=" N ASN D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 removed outlier: 3.665A pdb=" N ILE D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 217' Processing helix chain 'D' and resid 235 through 247 removed outlier: 3.514A pdb=" N LEU D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 272 removed outlier: 3.524A pdb=" N VAL D 272 " --> pdb=" O HIS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 287 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 333 through 337 removed outlier: 3.928A pdb=" N ARG D 336 " --> pdb=" O TYR D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 369 removed outlier: 3.768A pdb=" N LEU D 361 " --> pdb=" O SER D 357 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D 362 " --> pdb=" O HIS D 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 369 " --> pdb=" O PHE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 392 through 401 Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 414 through 417 Processing helix chain 'E' and resid 30 through 47 removed outlier: 3.650A pdb=" N PHE E 43 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR E 47 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 70 removed outlier: 3.966A pdb=" N LEU E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS E 70 " --> pdb=" O TRP E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.616A pdb=" N GLY E 89 " --> pdb=" O HIS E 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG E 90 " --> pdb=" O GLU E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 86 through 90' Processing helix chain 'E' and resid 144 through 160 removed outlier: 4.283A pdb=" N PHE E 148 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN E 149 " --> pdb=" O LYS E 145 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU E 157 " --> pdb=" O GLU E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 211 removed outlier: 3.835A pdb=" N ASN E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 217 removed outlier: 3.664A pdb=" N ILE E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 212 through 217' Processing helix chain 'E' and resid 235 through 247 removed outlier: 3.514A pdb=" N LEU E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 272 removed outlier: 3.524A pdb=" N VAL E 272 " --> pdb=" O HIS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 287 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 333 through 337 removed outlier: 3.928A pdb=" N ARG E 336 " --> pdb=" O TYR E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 369 removed outlier: 3.769A pdb=" N LEU E 361 " --> pdb=" O SER E 357 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR E 362 " --> pdb=" O HIS E 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR E 369 " --> pdb=" O PHE E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 388 Processing helix chain 'E' and resid 392 through 401 Processing helix chain 'E' and resid 406 through 413 Processing helix chain 'E' and resid 414 through 417 Processing helix chain 'F' and resid 30 through 47 removed outlier: 3.650A pdb=" N PHE F 43 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR F 47 " --> pdb=" O PHE F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 70 removed outlier: 3.967A pdb=" N LEU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS F 70 " --> pdb=" O TRP F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.616A pdb=" N GLY F 89 " --> pdb=" O HIS F 86 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 90' Processing helix chain 'F' and resid 144 through 160 removed outlier: 4.283A pdb=" N PHE F 148 " --> pdb=" O ARG F 144 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN F 149 " --> pdb=" O LYS F 145 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 157 " --> pdb=" O GLU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 211 removed outlier: 3.835A pdb=" N ASN F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 217 removed outlier: 3.664A pdb=" N ILE F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 212 through 217' Processing helix chain 'F' and resid 235 through 247 removed outlier: 3.513A pdb=" N LEU F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 272 removed outlier: 3.523A pdb=" N VAL F 272 " --> pdb=" O HIS F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 287 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 333 through 337 removed outlier: 3.927A pdb=" N ARG F 336 " --> pdb=" O TYR F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 369 removed outlier: 3.769A pdb=" N LEU F 361 " --> pdb=" O SER F 357 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR F 362 " --> pdb=" O HIS F 358 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR F 369 " --> pdb=" O PHE F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 392 through 401 Processing helix chain 'F' and resid 406 through 413 Processing helix chain 'F' and resid 414 through 417 Processing helix chain 'G' and resid 30 through 47 removed outlier: 3.650A pdb=" N PHE G 43 " --> pdb=" O GLY G 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR G 47 " --> pdb=" O PHE G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 70 removed outlier: 3.966A pdb=" N LEU G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG G 69 " --> pdb=" O SER G 65 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS G 70 " --> pdb=" O TRP G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 removed outlier: 3.616A pdb=" N GLY G 89 " --> pdb=" O HIS G 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG G 90 " --> pdb=" O GLU G 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 86 through 90' Processing helix chain 'G' and resid 144 through 160 removed outlier: 4.282A pdb=" N PHE G 148 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN G 149 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU G 157 " --> pdb=" O GLU G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 211 removed outlier: 3.836A pdb=" N ASN G 211 " --> pdb=" O GLU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 217 removed outlier: 3.664A pdb=" N ILE G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP G 217 " --> pdb=" O LYS G 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 212 through 217' Processing helix chain 'G' and resid 235 through 247 removed outlier: 3.513A pdb=" N LEU G 247 " --> pdb=" O LEU G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 272 removed outlier: 3.525A pdb=" N VAL G 272 " --> pdb=" O HIS G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 287 Processing helix chain 'G' and resid 312 through 316 Processing helix chain 'G' and resid 333 through 337 removed outlier: 3.928A pdb=" N ARG G 336 " --> pdb=" O TYR G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 369 removed outlier: 3.769A pdb=" N LEU G 361 " --> pdb=" O SER G 357 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR G 362 " --> pdb=" O HIS G 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR G 369 " --> pdb=" O PHE G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 388 Processing helix chain 'G' and resid 392 through 401 Processing helix chain 'G' and resid 406 through 413 Processing helix chain 'G' and resid 414 through 417 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 107 removed outlier: 3.565A pdb=" N GLY A 102 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 51 " --> pdb=" O LEU G 77 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N VAL G 79 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL A 53 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N THR G 81 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER G 82 " --> pdb=" O LYS G 94 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS G 94 " --> pdb=" O SER G 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 99 removed outlier: 3.681A pdb=" N LYS A 94 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER A 82 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A 77 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 79 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 102 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 6.746A pdb=" N TYR A 169 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER A 255 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ALA A 171 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 282 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER A 277 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N PHE A 328 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL A 279 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR A 330 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 281 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.848A pdb=" N LEU A 227 " --> pdb=" O GLU A 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 94 through 99 removed outlier: 3.682A pdb=" N LYS B 94 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER B 82 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 77 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 53 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 79 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 102 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 177 removed outlier: 6.746A pdb=" N TYR B 169 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER B 255 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ALA B 171 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 282 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER B 277 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE B 328 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL B 279 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR B 330 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 281 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 226 through 229 removed outlier: 6.849A pdb=" N LEU B 227 " --> pdb=" O GLU B 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 94 through 99 removed outlier: 3.682A pdb=" N LYS C 94 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER C 82 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU C 77 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 79 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D 102 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 175 through 177 removed outlier: 6.746A pdb=" N TYR C 169 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER C 255 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ALA C 171 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 282 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER C 277 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE C 328 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL C 279 " --> pdb=" O PHE C 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR C 330 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU C 281 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 226 through 229 removed outlier: 6.848A pdb=" N LEU C 227 " --> pdb=" O GLU C 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 94 through 99 removed outlier: 3.682A pdb=" N LYS D 94 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER D 82 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU D 77 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY E 102 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 175 through 177 removed outlier: 6.746A pdb=" N TYR D 169 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER D 255 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ALA D 171 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 282 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER D 277 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE D 328 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL D 279 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR D 330 " --> pdb=" O VAL D 279 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU D 281 " --> pdb=" O THR D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 226 through 229 removed outlier: 6.849A pdb=" N LEU D 227 " --> pdb=" O GLU D 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 94 through 99 removed outlier: 3.682A pdb=" N LYS E 94 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER E 82 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 77 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F 53 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 79 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY F 102 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 175 through 177 removed outlier: 6.746A pdb=" N TYR E 169 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N SER E 255 " --> pdb=" O TYR E 169 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ALA E 171 " --> pdb=" O SER E 255 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU E 282 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N SER E 277 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE E 328 " --> pdb=" O SER E 277 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL E 279 " --> pdb=" O PHE E 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR E 330 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU E 281 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 226 through 229 removed outlier: 6.849A pdb=" N LEU E 227 " --> pdb=" O GLU E 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 94 through 99 removed outlier: 3.681A pdb=" N LYS F 94 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER F 82 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU F 77 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL F 79 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY G 102 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 175 through 177 removed outlier: 6.746A pdb=" N TYR F 169 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER F 255 " --> pdb=" O TYR F 169 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ALA F 171 " --> pdb=" O SER F 255 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU F 282 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER F 277 " --> pdb=" O ILE F 326 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE F 328 " --> pdb=" O SER F 277 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL F 279 " --> pdb=" O PHE F 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR F 330 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU F 281 " --> pdb=" O THR F 330 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 226 through 229 removed outlier: 6.848A pdb=" N LEU F 227 " --> pdb=" O GLU F 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 175 through 177 removed outlier: 6.746A pdb=" N TYR G 169 " --> pdb=" O LEU G 253 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER G 255 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ALA G 171 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU G 282 " --> pdb=" O LEU G 254 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER G 277 " --> pdb=" O ILE G 326 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE G 328 " --> pdb=" O SER G 277 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL G 279 " --> pdb=" O PHE G 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR G 330 " --> pdb=" O VAL G 279 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU G 281 " --> pdb=" O THR G 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 226 through 229 removed outlier: 6.849A pdb=" N LEU G 227 " --> pdb=" O GLU G 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 768 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.82 Time building geometry restraints manager: 5.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 20411 1.01 - 1.21: 22 1.21 - 1.41: 8995 1.41 - 1.61: 12068 1.61 - 1.81: 147 Bond restraints: 41643 Sorted by residual: bond pdb=" CG MET G 31 " pdb=" HG2 MET G 31 " ideal model delta sigma weight residual 0.970 1.036 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" CD ARG G 33 " pdb=" HD3 ARG G 33 " ideal model delta sigma weight residual 0.970 0.923 0.047 2.00e-02 2.50e+03 5.64e+00 bond pdb=" CD ARG E 33 " pdb=" HD2 ARG E 33 " ideal model delta sigma weight residual 0.970 1.011 -0.041 2.00e-02 2.50e+03 4.10e+00 bond pdb=" CE MET E 31 " pdb=" HE2 MET E 31 " ideal model delta sigma weight residual 0.970 1.008 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" CD ARG E 33 " pdb=" HD3 ARG E 33 " ideal model delta sigma weight residual 0.970 1.008 -0.038 2.00e-02 2.50e+03 3.62e+00 ... (remaining 41638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.97: 74919 10.97 - 21.93: 41 21.93 - 32.90: 11 32.90 - 43.87: 5 43.87 - 54.83: 1 Bond angle restraints: 74977 Sorted by residual: angle pdb=" NE ARG G 33 " pdb=" CD ARG G 33 " pdb=" HD3 ARG G 33 " ideal model delta sigma weight residual 108.00 53.17 54.83 3.00e+00 1.11e-01 3.34e+02 angle pdb=" CG ARG G 33 " pdb=" CD ARG G 33 " pdb=" HD3 ARG G 33 " ideal model delta sigma weight residual 109.00 66.49 42.51 3.00e+00 1.11e-01 2.01e+02 angle pdb=" NZ LYS C 34 " pdb=" CE LYS C 34 " pdb=" HE3 LYS C 34 " ideal model delta sigma weight residual 108.00 66.98 41.02 3.00e+00 1.11e-01 1.87e+02 angle pdb=" CD LYS C 34 " pdb=" CE LYS C 34 " pdb=" HE3 LYS C 34 " ideal model delta sigma weight residual 109.00 69.71 39.29 3.00e+00 1.11e-01 1.71e+02 angle pdb=" SD MET E 31 " pdb=" CE MET E 31 " pdb=" HE1 MET E 31 " ideal model delta sigma weight residual 109.00 72.04 36.96 3.00e+00 1.11e-01 1.52e+02 ... (remaining 74972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 17457 17.47 - 34.95: 1588 34.95 - 52.42: 428 52.42 - 69.89: 106 69.89 - 87.36: 28 Dihedral angle restraints: 19607 sinusoidal: 10584 harmonic: 9023 Sorted by residual: dihedral pdb=" CA TYR G 108 " pdb=" C TYR G 108 " pdb=" N GLN G 109 " pdb=" CA GLN G 109 " ideal model delta harmonic sigma weight residual 180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA TYR B 108 " pdb=" C TYR B 108 " pdb=" N GLN B 109 " pdb=" CA GLN B 109 " ideal model delta harmonic sigma weight residual -180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA TYR C 108 " pdb=" C TYR C 108 " pdb=" N GLN C 109 " pdb=" CA GLN C 109 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 19604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1927 0.037 - 0.074: 836 0.074 - 0.110: 278 0.110 - 0.147: 67 0.147 - 0.184: 14 Chirality restraints: 3122 Sorted by residual: chirality pdb=" CA ILE A 98 " pdb=" N ILE A 98 " pdb=" C ILE A 98 " pdb=" CB ILE A 98 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA ILE D 98 " pdb=" N ILE D 98 " pdb=" C ILE D 98 " pdb=" CB ILE D 98 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA ILE G 98 " pdb=" N ILE G 98 " pdb=" C ILE G 98 " pdb=" CB ILE G 98 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.25e-01 ... (remaining 3119 not shown) Planarity restraints: 6132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 53 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.34e+00 pdb=" N PRO G 54 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO G 54 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO G 54 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 53 " 0.048 5.00e-02 4.00e+02 7.22e-02 8.33e+00 pdb=" N PRO E 54 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO E 54 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 54 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 53 " 0.048 5.00e-02 4.00e+02 7.21e-02 8.32e+00 pdb=" N PRO D 54 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 54 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 54 " 0.040 5.00e-02 4.00e+02 ... (remaining 6129 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 1112 2.14 - 2.76: 75371 2.76 - 3.37: 105689 3.37 - 3.99: 126527 3.99 - 4.60: 200887 Nonbonded interactions: 509586 Sorted by model distance: nonbonded pdb=" HE3 LYS C 34 " pdb=" HZ1 LYS C 34 " model vdw 1.530 1.816 nonbonded pdb=" HE2 LYS A 34 " pdb=" HZ1 LYS A 34 " model vdw 1.618 1.816 nonbonded pdb=" HD3 ARG G 33 " pdb=" HE ARG G 33 " model vdw 1.634 1.816 nonbonded pdb=" HD2 LYS C 34 " pdb=" HE3 LYS C 34 " model vdw 1.640 1.952 nonbonded pdb=" O VAL F 384 " pdb=" HG1 THR F 388 " model vdw 1.685 2.450 ... (remaining 509581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.250 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 38.280 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 21210 Z= 0.337 Angle : 0.867 14.521 28763 Z= 0.443 Chirality : 0.046 0.184 3122 Planarity : 0.006 0.072 3696 Dihedral : 14.311 87.363 7805 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 0.95 % Allowed : 3.89 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.15), residues: 2541 helix: -2.24 (0.13), residues: 931 sheet: -2.62 (0.18), residues: 595 loop : -2.91 (0.21), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 119 TYR 0.018 0.002 TYR D 60 PHE 0.016 0.002 PHE D 400 TRP 0.012 0.002 TRP A 214 HIS 0.009 0.002 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00789 (21210) covalent geometry : angle 0.86700 (28763) hydrogen bonds : bond 0.13225 ( 768) hydrogen bonds : angle 5.99031 ( 2178) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 555 time to evaluate : 1.154 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.5917 (m-80) cc_final: 0.5093 (m-80) REVERT: A 80 GLU cc_start: 0.6908 (tt0) cc_final: 0.6576 (mt-10) REVERT: A 92 SER cc_start: 0.8521 (m) cc_final: 0.8319 (t) REVERT: A 132 TRP cc_start: 0.7194 (t60) cc_final: 0.5652 (t-100) REVERT: A 168 MET cc_start: 0.7856 (tpp) cc_final: 0.7475 (tpp) REVERT: A 189 ASP cc_start: 0.8612 (m-30) cc_final: 0.8024 (p0) REVERT: A 222 TYR cc_start: 0.7490 (t80) cc_final: 0.6948 (t80) REVERT: A 227 LEU cc_start: 0.9046 (tt) cc_final: 0.8743 (tp) REVERT: A 360 GLN cc_start: 0.7964 (tt0) cc_final: 0.7719 (tt0) REVERT: A 379 ASN cc_start: 0.7771 (t0) cc_final: 0.7388 (t0) REVERT: A 413 ASN cc_start: 0.7045 (m110) cc_final: 0.6643 (m110) REVERT: B 80 GLU cc_start: 0.7382 (tt0) cc_final: 0.6970 (mt-10) REVERT: B 98 ILE cc_start: 0.8235 (mt) cc_final: 0.7996 (mm) REVERT: B 116 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6813 (mt-10) REVERT: B 162 GLU cc_start: 0.7424 (tp30) cc_final: 0.7142 (tp30) REVERT: B 189 ASP cc_start: 0.8817 (m-30) cc_final: 0.8203 (p0) REVERT: B 248 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 360 GLN cc_start: 0.7779 (tt0) cc_final: 0.7532 (tt0) REVERT: B 413 ASN cc_start: 0.7775 (m110) cc_final: 0.7541 (m110) REVERT: C 45 ARG cc_start: 0.6965 (mmp-170) cc_final: 0.5175 (ptm160) REVERT: C 77 LEU cc_start: 0.7565 (pt) cc_final: 0.7331 (pp) REVERT: C 116 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7225 (mt-10) REVERT: C 125 ASP cc_start: 0.6920 (m-30) cc_final: 0.6482 (t0) REVERT: C 133 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7536 (mt-10) REVERT: C 189 ASP cc_start: 0.8848 (m-30) cc_final: 0.8182 (p0) REVERT: C 222 TYR cc_start: 0.7550 (t80) cc_final: 0.7248 (t80) REVERT: C 359 TRP cc_start: 0.7885 (t60) cc_final: 0.7561 (t-100) REVERT: C 379 ASN cc_start: 0.8324 (t0) cc_final: 0.7949 (t0) REVERT: C 382 GLU cc_start: 0.8179 (tp30) cc_final: 0.7867 (tp30) REVERT: C 408 MET cc_start: 0.8135 (mtt) cc_final: 0.7774 (mtt) REVERT: D 31 MET cc_start: -0.0223 (OUTLIER) cc_final: -0.0575 (mpp) REVERT: D 45 ARG cc_start: 0.7015 (mmp-170) cc_final: 0.5061 (ttm170) REVERT: D 80 GLU cc_start: 0.7290 (tt0) cc_final: 0.6809 (mt-10) REVERT: D 96 GLU cc_start: 0.5962 (tt0) cc_final: 0.5681 (tt0) REVERT: D 181 TYR cc_start: 0.8071 (m-10) cc_final: 0.7763 (m-80) REVERT: D 189 ASP cc_start: 0.8554 (m-30) cc_final: 0.7942 (p0) REVERT: D 379 ASN cc_start: 0.7783 (t0) cc_final: 0.7425 (t0) REVERT: E 47 TYR cc_start: 0.5947 (m-80) cc_final: 0.5526 (m-80) REVERT: E 77 LEU cc_start: 0.7689 (pt) cc_final: 0.7436 (pp) REVERT: E 80 GLU cc_start: 0.6825 (tt0) cc_final: 0.6583 (mt-10) REVERT: E 92 SER cc_start: 0.8374 (m) cc_final: 0.7926 (t) REVERT: E 116 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6967 (mt-10) REVERT: E 145 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7485 (tptp) REVERT: E 189 ASP cc_start: 0.8550 (m-30) cc_final: 0.7533 (p0) REVERT: E 223 ARG cc_start: 0.7729 (ttm170) cc_final: 0.6978 (mtm180) REVERT: E 234 CYS cc_start: 0.8454 (t) cc_final: 0.8074 (t) REVERT: E 401 MET cc_start: 0.7426 (ttt) cc_final: 0.7044 (ttt) REVERT: E 404 LYS cc_start: 0.7273 (mmtt) cc_final: 0.6894 (mmtt) REVERT: E 413 ASN cc_start: 0.8059 (m110) cc_final: 0.7716 (m110) REVERT: F 31 MET cc_start: 0.1880 (OUTLIER) cc_final: 0.1353 (mtm) REVERT: F 45 ARG cc_start: 0.7088 (mmp-170) cc_final: 0.5247 (ttp-170) REVERT: F 47 TYR cc_start: 0.6317 (m-80) cc_final: 0.4918 (m-80) REVERT: F 49 ILE cc_start: 0.8020 (mt) cc_final: 0.7784 (tt) REVERT: F 80 GLU cc_start: 0.7275 (tt0) cc_final: 0.6978 (mt-10) REVERT: F 98 ILE cc_start: 0.8456 (mt) cc_final: 0.8203 (mm) REVERT: F 108 TYR cc_start: 0.8276 (t80) cc_final: 0.8032 (t80) REVERT: F 134 SER cc_start: 0.8291 (m) cc_final: 0.8080 (t) REVERT: F 143 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7323 (m-30) REVERT: F 162 GLU cc_start: 0.6946 (tp30) cc_final: 0.6744 (tp30) REVERT: F 177 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7220 (mtt-85) REVERT: F 189 ASP cc_start: 0.8682 (m-30) cc_final: 0.7974 (p0) REVERT: F 213 LYS cc_start: 0.8131 (tptp) cc_final: 0.7441 (tptp) REVERT: F 234 CYS cc_start: 0.8072 (t) cc_final: 0.7779 (t) REVERT: F 279 VAL cc_start: 0.8622 (m) cc_final: 0.8274 (p) REVERT: F 356 CYS cc_start: 0.8139 (m) cc_final: 0.7830 (m) REVERT: F 365 PHE cc_start: 0.7718 (t80) cc_final: 0.7329 (t80) REVERT: F 390 GLU cc_start: 0.8309 (pm20) cc_final: 0.7909 (pm20) REVERT: F 413 ASN cc_start: 0.7895 (m110) cc_final: 0.7542 (m110) REVERT: G 31 MET cc_start: 0.0590 (OUTLIER) cc_final: 0.0119 (mpp) REVERT: G 45 ARG cc_start: 0.7061 (mmp-170) cc_final: 0.6322 (mmm160) REVERT: G 47 TYR cc_start: 0.6569 (m-80) cc_final: 0.5250 (m-80) REVERT: G 116 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7248 (mt-10) REVERT: G 134 SER cc_start: 0.8362 (m) cc_final: 0.7982 (p) REVERT: G 177 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7816 (mmm-85) REVERT: G 189 ASP cc_start: 0.8824 (m-30) cc_final: 0.8204 (p0) REVERT: G 217 ASP cc_start: 0.8148 (m-30) cc_final: 0.7830 (m-30) REVERT: G 356 CYS cc_start: 0.7679 (m) cc_final: 0.7344 (m) REVERT: G 413 ASN cc_start: 0.8472 (m110) cc_final: 0.8174 (m110) outliers start: 21 outliers final: 3 residues processed: 556 average time/residue: 0.4308 time to fit residues: 335.6844 Evaluate side-chains 458 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 451 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain F residue 31 MET Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain G residue 31 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 30.0000 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 412 HIS B 46 HIS B 412 HIS C 412 HIS D 412 HIS D 413 ASN E 412 HIS F 412 HIS G 412 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.136518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102833 restraints weight = 94981.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108093 restraints weight = 42416.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111630 restraints weight = 24473.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113879 restraints weight = 16771.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.115380 restraints weight = 13064.250| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21210 Z= 0.125 Angle : 0.561 5.605 28763 Z= 0.294 Chirality : 0.039 0.172 3122 Planarity : 0.006 0.064 3696 Dihedral : 5.909 59.726 2887 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.18 % Allowed : 12.34 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.17), residues: 2541 helix: -0.56 (0.16), residues: 917 sheet: -1.70 (0.20), residues: 567 loop : -2.61 (0.21), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 223 TYR 0.014 0.001 TYR G 83 PHE 0.016 0.002 PHE F 179 TRP 0.014 0.001 TRP E 132 HIS 0.006 0.001 HIS F 86 Details of bonding type rmsd covalent geometry : bond 0.00283 (21210) covalent geometry : angle 0.56056 (28763) hydrogen bonds : bond 0.03646 ( 768) hydrogen bonds : angle 4.68027 ( 2178) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 462 time to evaluate : 0.919 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.6026 (m-80) cc_final: 0.5536 (m-80) REVERT: A 80 GLU cc_start: 0.6861 (tt0) cc_final: 0.6596 (mt-10) REVERT: A 92 SER cc_start: 0.8624 (m) cc_final: 0.8292 (t) REVERT: A 189 ASP cc_start: 0.8496 (m-30) cc_final: 0.7928 (p0) REVERT: A 213 LYS cc_start: 0.8388 (tptp) cc_final: 0.8152 (tptp) REVERT: A 222 TYR cc_start: 0.7498 (t80) cc_final: 0.6975 (t80) REVERT: A 379 ASN cc_start: 0.7822 (t0) cc_final: 0.7471 (t0) REVERT: A 390 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: B 47 TYR cc_start: 0.5963 (m-80) cc_final: 0.5052 (m-80) REVERT: B 80 GLU cc_start: 0.7407 (tt0) cc_final: 0.6953 (mt-10) REVERT: B 113 ILE cc_start: 0.8209 (mt) cc_final: 0.7981 (mm) REVERT: B 162 GLU cc_start: 0.7344 (tp30) cc_final: 0.7132 (tp30) REVERT: B 177 ARG cc_start: 0.7848 (mmm-85) cc_final: 0.7188 (mtt-85) REVERT: B 189 ASP cc_start: 0.8823 (m-30) cc_final: 0.7998 (p0) REVERT: B 218 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7259 (mtm180) REVERT: B 248 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7782 (mm-30) REVERT: B 332 ASN cc_start: 0.8470 (m-40) cc_final: 0.8245 (m-40) REVERT: B 346 ARG cc_start: 0.8225 (mtp180) cc_final: 0.8019 (mtp180) REVERT: B 360 GLN cc_start: 0.7650 (tt0) cc_final: 0.7281 (tt0) REVERT: B 382 GLU cc_start: 0.7565 (tp30) cc_final: 0.7261 (tp30) REVERT: C 133 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7519 (mt-10) REVERT: C 168 MET cc_start: 0.8200 (tpp) cc_final: 0.7981 (tpp) REVERT: C 189 ASP cc_start: 0.8776 (m-30) cc_final: 0.8004 (p0) REVERT: C 218 ARG cc_start: 0.8355 (mmt90) cc_final: 0.8061 (mmt90) REVERT: C 222 TYR cc_start: 0.7543 (t80) cc_final: 0.7284 (t80) REVERT: C 240 ILE cc_start: 0.8618 (mm) cc_final: 0.8389 (mm) REVERT: C 248 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7336 (mm-30) REVERT: C 359 TRP cc_start: 0.7995 (t60) cc_final: 0.7629 (t-100) REVERT: C 360 GLN cc_start: 0.7310 (tt0) cc_final: 0.7107 (tt0) REVERT: C 379 ASN cc_start: 0.8052 (t0) cc_final: 0.7786 (t0) REVERT: C 382 GLU cc_start: 0.7847 (tp30) cc_final: 0.7583 (tp30) REVERT: C 408 MET cc_start: 0.8099 (mtt) cc_final: 0.7693 (mtt) REVERT: D 31 MET cc_start: -0.0114 (OUTLIER) cc_final: -0.0442 (mpp) REVERT: D 80 GLU cc_start: 0.7131 (tt0) cc_final: 0.6749 (mt-10) REVERT: D 189 ASP cc_start: 0.8507 (m-30) cc_final: 0.7934 (p0) REVERT: D 379 ASN cc_start: 0.7716 (t0) cc_final: 0.7417 (t0) REVERT: E 47 TYR cc_start: 0.5839 (m-80) cc_final: 0.5290 (m-80) REVERT: E 80 GLU cc_start: 0.6893 (tt0) cc_final: 0.6674 (mt-10) REVERT: E 92 SER cc_start: 0.8563 (m) cc_final: 0.8223 (t) REVERT: E 116 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6901 (mt-10) REVERT: E 189 ASP cc_start: 0.8484 (m-30) cc_final: 0.7473 (p0) REVERT: E 218 ARG cc_start: 0.7913 (mtt180) cc_final: 0.7552 (mtm180) REVERT: E 223 ARG cc_start: 0.7591 (ttm170) cc_final: 0.7134 (mtm180) REVERT: E 234 CYS cc_start: 0.8007 (t) cc_final: 0.7711 (t) REVERT: E 264 ASP cc_start: 0.7959 (p0) cc_final: 0.7321 (t70) REVERT: E 329 MET cc_start: 0.8710 (mtm) cc_final: 0.8504 (mtm) REVERT: E 401 MET cc_start: 0.7674 (ttt) cc_final: 0.7272 (ttt) REVERT: F 47 TYR cc_start: 0.6513 (m-80) cc_final: 0.5343 (m-80) REVERT: F 49 ILE cc_start: 0.7986 (mt) cc_final: 0.7605 (tt) REVERT: F 73 ARG cc_start: 0.7529 (mmt180) cc_final: 0.7122 (mmt180) REVERT: F 80 GLU cc_start: 0.7516 (tt0) cc_final: 0.7229 (mt-10) REVERT: F 98 ILE cc_start: 0.8737 (mt) cc_final: 0.8466 (mm) REVERT: F 134 SER cc_start: 0.8331 (m) cc_final: 0.8126 (t) REVERT: F 143 ASP cc_start: 0.7299 (m-30) cc_final: 0.7088 (m-30) REVERT: F 162 GLU cc_start: 0.7034 (tp30) cc_final: 0.6802 (tp30) REVERT: F 177 ARG cc_start: 0.7716 (mmm-85) cc_final: 0.7340 (mmt90) REVERT: F 189 ASP cc_start: 0.8640 (m-30) cc_final: 0.7967 (p0) REVERT: F 213 LYS cc_start: 0.8101 (tptp) cc_final: 0.7369 (tptp) REVERT: F 234 CYS cc_start: 0.7665 (t) cc_final: 0.7277 (t) REVERT: F 279 VAL cc_start: 0.8843 (m) cc_final: 0.8459 (p) REVERT: F 378 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8670 (mt-10) REVERT: F 413 ASN cc_start: 0.7991 (m110) cc_final: 0.7628 (m110) REVERT: G 31 MET cc_start: 0.0878 (OUTLIER) cc_final: 0.0405 (mpp) REVERT: G 45 ARG cc_start: 0.7309 (mmp-170) cc_final: 0.5789 (ttp-170) REVERT: G 47 TYR cc_start: 0.6299 (m-80) cc_final: 0.5051 (m-80) REVERT: G 123 MET cc_start: 0.5922 (ptm) cc_final: 0.5680 (ptm) REVERT: G 177 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.7805 (mmm-85) REVERT: G 189 ASP cc_start: 0.8811 (m-30) cc_final: 0.8147 (p0) REVERT: G 413 ASN cc_start: 0.8180 (m110) cc_final: 0.7975 (m110) outliers start: 26 outliers final: 15 residues processed: 474 average time/residue: 0.4135 time to fit residues: 277.6989 Evaluate side-chains 454 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 436 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain G residue 31 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 111 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 72 optimal weight: 30.0000 chunk 126 optimal weight: 1.9990 chunk 227 optimal weight: 0.3980 chunk 122 optimal weight: 0.8980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN B 46 HIS C 413 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099665 restraints weight = 95283.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104756 restraints weight = 42849.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108182 restraints weight = 25018.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110402 restraints weight = 17336.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111879 restraints weight = 13583.825| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21210 Z= 0.167 Angle : 0.544 5.470 28763 Z= 0.291 Chirality : 0.038 0.164 3122 Planarity : 0.005 0.066 3696 Dihedral : 5.341 54.830 2878 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 0.95 % Allowed : 14.20 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.17), residues: 2541 helix: 0.26 (0.17), residues: 917 sheet: -1.49 (0.21), residues: 560 loop : -2.47 (0.21), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 223 TYR 0.024 0.002 TYR B 47 PHE 0.018 0.002 PHE F 179 TRP 0.014 0.001 TRP E 132 HIS 0.009 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00380 (21210) covalent geometry : angle 0.54393 (28763) hydrogen bonds : bond 0.03487 ( 768) hydrogen bonds : angle 4.43207 ( 2178) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 448 time to evaluate : 0.991 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.6019 (m-80) cc_final: 0.5532 (m-80) REVERT: A 80 GLU cc_start: 0.6895 (tt0) cc_final: 0.6591 (mt-10) REVERT: A 92 SER cc_start: 0.8672 (m) cc_final: 0.8285 (t) REVERT: A 132 TRP cc_start: 0.7583 (t60) cc_final: 0.5802 (t-100) REVERT: A 186 ARG cc_start: 0.8551 (mtt180) cc_final: 0.8241 (ptp90) REVERT: A 189 ASP cc_start: 0.8362 (m-30) cc_final: 0.7945 (p0) REVERT: A 236 LYS cc_start: 0.8640 (mtmm) cc_final: 0.8341 (mttt) REVERT: A 248 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7743 (mm-30) REVERT: A 379 ASN cc_start: 0.7640 (t0) cc_final: 0.7373 (t0) REVERT: A 390 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: B 47 TYR cc_start: 0.5808 (m-80) cc_final: 0.4986 (m-80) REVERT: B 113 ILE cc_start: 0.8266 (mt) cc_final: 0.8052 (mm) REVERT: B 177 ARG cc_start: 0.7763 (mmm-85) cc_final: 0.7083 (mtt-85) REVERT: B 189 ASP cc_start: 0.8795 (m-30) cc_final: 0.7956 (p0) REVERT: B 248 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7792 (mm-30) REVERT: B 346 ARG cc_start: 0.8103 (mtp180) cc_final: 0.7797 (mtp180) REVERT: B 360 GLN cc_start: 0.7792 (tt0) cc_final: 0.7187 (tt0) REVERT: B 382 GLU cc_start: 0.7597 (tp30) cc_final: 0.7269 (tp30) REVERT: C 133 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7654 (mm-30) REVERT: C 189 ASP cc_start: 0.8748 (m-30) cc_final: 0.8201 (p0) REVERT: C 222 TYR cc_start: 0.7516 (t80) cc_final: 0.7292 (t80) REVERT: C 240 ILE cc_start: 0.8618 (mm) cc_final: 0.8392 (mm) REVERT: C 248 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7531 (mm-30) REVERT: C 359 TRP cc_start: 0.8091 (t60) cc_final: 0.7887 (t-100) REVERT: C 379 ASN cc_start: 0.8042 (t0) cc_final: 0.7703 (t0) REVERT: C 382 GLU cc_start: 0.7941 (tp30) cc_final: 0.7695 (tp30) REVERT: C 408 MET cc_start: 0.8035 (mtt) cc_final: 0.7637 (mtt) REVERT: D 31 MET cc_start: 0.0069 (OUTLIER) cc_final: -0.0337 (mpp) REVERT: D 80 GLU cc_start: 0.7076 (tt0) cc_final: 0.6734 (mt-10) REVERT: D 168 MET cc_start: 0.8036 (ttm) cc_final: 0.7807 (ttm) REVERT: D 189 ASP cc_start: 0.8379 (m-30) cc_final: 0.7933 (p0) REVERT: D 379 ASN cc_start: 0.7770 (t0) cc_final: 0.7485 (t0) REVERT: E 80 GLU cc_start: 0.7080 (tt0) cc_final: 0.6841 (mt-10) REVERT: E 92 SER cc_start: 0.8360 (m) cc_final: 0.8046 (t) REVERT: E 116 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7101 (mt-10) REVERT: E 177 ARG cc_start: 0.7844 (mmm-85) cc_final: 0.7266 (mmt90) REVERT: E 189 ASP cc_start: 0.8479 (m-30) cc_final: 0.7454 (p0) REVERT: E 223 ARG cc_start: 0.7663 (ttm170) cc_final: 0.7204 (mtm180) REVERT: E 264 ASP cc_start: 0.8068 (p0) cc_final: 0.7368 (t70) REVERT: E 401 MET cc_start: 0.7673 (ttt) cc_final: 0.7391 (ttt) REVERT: F 80 GLU cc_start: 0.7610 (tt0) cc_final: 0.7226 (mt-10) REVERT: F 108 TYR cc_start: 0.7913 (t80) cc_final: 0.7357 (t80) REVERT: F 134 SER cc_start: 0.8465 (m) cc_final: 0.8055 (p) REVERT: F 177 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7334 (mmt90) REVERT: F 189 ASP cc_start: 0.8622 (m-30) cc_final: 0.7941 (p0) REVERT: F 234 CYS cc_start: 0.7657 (t) cc_final: 0.7284 (t) REVERT: F 390 GLU cc_start: 0.8191 (pm20) cc_final: 0.7797 (pm20) REVERT: F 413 ASN cc_start: 0.8107 (m110) cc_final: 0.7868 (m110) REVERT: G 45 ARG cc_start: 0.7433 (mmp-170) cc_final: 0.5351 (ttp-170) REVERT: G 47 TYR cc_start: 0.6151 (m-80) cc_final: 0.5048 (m-80) REVERT: G 123 MET cc_start: 0.6506 (ptm) cc_final: 0.6185 (ptm) REVERT: G 177 ARG cc_start: 0.7829 (mmm-85) cc_final: 0.7594 (mmm-85) REVERT: G 189 ASP cc_start: 0.8820 (m-30) cc_final: 0.8146 (p0) REVERT: G 218 ARG cc_start: 0.8230 (mmt90) cc_final: 0.8003 (mtt90) outliers start: 21 outliers final: 17 residues processed: 454 average time/residue: 0.4050 time to fit residues: 261.6682 Evaluate side-chains 443 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 424 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 413 ASN Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain F residue 31 MET Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 376 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 173 optimal weight: 0.0070 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.099331 restraints weight = 94586.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104403 restraints weight = 42773.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107855 restraints weight = 25116.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110074 restraints weight = 17454.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111542 restraints weight = 13698.934| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21210 Z= 0.147 Angle : 0.522 5.923 28763 Z= 0.278 Chirality : 0.038 0.167 3122 Planarity : 0.005 0.064 3696 Dihedral : 5.090 50.432 2873 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.67 % Allowed : 15.10 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.18), residues: 2541 helix: 0.63 (0.17), residues: 924 sheet: -1.21 (0.22), residues: 560 loop : -2.33 (0.21), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 223 TYR 0.015 0.001 TYR A 60 PHE 0.016 0.002 PHE F 179 TRP 0.012 0.001 TRP E 132 HIS 0.011 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00333 (21210) covalent geometry : angle 0.52224 (28763) hydrogen bonds : bond 0.03095 ( 768) hydrogen bonds : angle 4.23530 ( 2178) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 436 time to evaluate : 1.109 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6864 (tt0) cc_final: 0.6540 (mt-10) REVERT: A 92 SER cc_start: 0.8665 (m) cc_final: 0.8185 (t) REVERT: A 186 ARG cc_start: 0.8527 (mtt180) cc_final: 0.8226 (ptp90) REVERT: A 189 ASP cc_start: 0.8350 (m-30) cc_final: 0.7950 (p0) REVERT: A 236 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8381 (mttt) REVERT: A 379 ASN cc_start: 0.7647 (t0) cc_final: 0.7405 (t0) REVERT: A 390 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.8022 (pm20) REVERT: B 47 TYR cc_start: 0.5955 (m-80) cc_final: 0.5498 (m-80) REVERT: B 125 ASP cc_start: 0.6481 (m-30) cc_final: 0.5494 (t0) REVERT: B 177 ARG cc_start: 0.7831 (mmm-85) cc_final: 0.7177 (mtt-85) REVERT: B 189 ASP cc_start: 0.8762 (m-30) cc_final: 0.7892 (p0) REVERT: B 223 ARG cc_start: 0.7723 (ttp-110) cc_final: 0.7379 (ttp-110) REVERT: B 248 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7782 (mm-30) REVERT: B 382 GLU cc_start: 0.7560 (tp30) cc_final: 0.7232 (tp30) REVERT: C 189 ASP cc_start: 0.8981 (m-30) cc_final: 0.8053 (p0) REVERT: C 222 TYR cc_start: 0.7612 (t80) cc_final: 0.7377 (t80) REVERT: C 229 TYR cc_start: 0.8330 (p90) cc_final: 0.8129 (p90) REVERT: C 240 ILE cc_start: 0.8625 (mm) cc_final: 0.8380 (mm) REVERT: C 248 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8122 (mm-30) REVERT: C 359 TRP cc_start: 0.8377 (t60) cc_final: 0.8112 (t-100) REVERT: C 379 ASN cc_start: 0.7894 (t0) cc_final: 0.7531 (t0) REVERT: C 382 GLU cc_start: 0.7900 (tp30) cc_final: 0.7653 (tp30) REVERT: C 408 MET cc_start: 0.7999 (mtt) cc_final: 0.7611 (mtt) REVERT: D 80 GLU cc_start: 0.7050 (tt0) cc_final: 0.6635 (mt-10) REVERT: D 168 MET cc_start: 0.7988 (ttm) cc_final: 0.7621 (ttm) REVERT: D 189 ASP cc_start: 0.8344 (m-30) cc_final: 0.7938 (p0) REVERT: D 379 ASN cc_start: 0.7580 (t0) cc_final: 0.7275 (t0) REVERT: E 47 TYR cc_start: 0.4885 (m-80) cc_final: 0.4525 (m-80) REVERT: E 92 SER cc_start: 0.8383 (m) cc_final: 0.8095 (t) REVERT: E 94 LYS cc_start: 0.8440 (tttp) cc_final: 0.8132 (tttt) REVERT: E 116 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7104 (mt-10) REVERT: E 189 ASP cc_start: 0.8479 (m-30) cc_final: 0.7450 (p0) REVERT: E 218 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7657 (mtm180) REVERT: E 223 ARG cc_start: 0.7669 (ttm170) cc_final: 0.7319 (mtm180) REVERT: E 401 MET cc_start: 0.7621 (ttt) cc_final: 0.7360 (ttt) REVERT: F 73 ARG cc_start: 0.7458 (mmt180) cc_final: 0.7107 (mmt180) REVERT: F 80 GLU cc_start: 0.7581 (tt0) cc_final: 0.7214 (mt-10) REVERT: F 125 ASP cc_start: 0.5863 (m-30) cc_final: 0.5584 (t70) REVERT: F 134 SER cc_start: 0.8456 (m) cc_final: 0.8105 (p) REVERT: F 177 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7380 (mmt90) REVERT: F 189 ASP cc_start: 0.8622 (m-30) cc_final: 0.7932 (p0) REVERT: F 234 CYS cc_start: 0.7497 (t) cc_final: 0.7162 (t) REVERT: F 365 PHE cc_start: 0.7242 (t80) cc_final: 0.6814 (t80) REVERT: F 413 ASN cc_start: 0.8153 (m110) cc_final: 0.7948 (m110) REVERT: G 45 ARG cc_start: 0.7521 (mmp-170) cc_final: 0.5393 (ttp-170) REVERT: G 47 TYR cc_start: 0.6240 (m-80) cc_final: 0.5149 (m-80) REVERT: G 116 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7219 (mt-10) REVERT: G 177 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7596 (mmm-85) REVERT: G 189 ASP cc_start: 0.8812 (m-30) cc_final: 0.8137 (p0) outliers start: 37 outliers final: 26 residues processed: 455 average time/residue: 0.4079 time to fit residues: 265.8018 Evaluate side-chains 445 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 418 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 399 TYR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain F residue 31 MET Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 134 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 8 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.134219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100918 restraints weight = 94356.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105799 restraints weight = 43761.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109070 restraints weight = 26114.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111221 restraints weight = 18425.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112570 restraints weight = 14594.996| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21210 Z= 0.132 Angle : 0.508 6.347 28763 Z= 0.270 Chirality : 0.038 0.166 3122 Planarity : 0.005 0.064 3696 Dihedral : 4.717 21.336 2870 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 1.08 % Allowed : 16.46 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.18), residues: 2541 helix: 0.94 (0.18), residues: 924 sheet: -1.08 (0.22), residues: 560 loop : -2.23 (0.22), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 177 TYR 0.015 0.001 TYR G 83 PHE 0.015 0.001 PHE G 179 TRP 0.011 0.001 TRP E 132 HIS 0.007 0.001 HIS F 86 Details of bonding type rmsd covalent geometry : bond 0.00302 (21210) covalent geometry : angle 0.50803 (28763) hydrogen bonds : bond 0.02919 ( 768) hydrogen bonds : angle 4.07884 ( 2178) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 431 time to evaluate : 0.908 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 SER cc_start: 0.9255 (m) cc_final: 0.8665 (t) REVERT: A 186 ARG cc_start: 0.8519 (mtt180) cc_final: 0.8227 (ptp90) REVERT: A 189 ASP cc_start: 0.8370 (m-30) cc_final: 0.7932 (p0) REVERT: A 213 LYS cc_start: 0.8185 (tptp) cc_final: 0.7956 (tptp) REVERT: A 220 ILE cc_start: 0.9051 (mm) cc_final: 0.8848 (mm) REVERT: A 379 ASN cc_start: 0.7708 (t0) cc_final: 0.7430 (t0) REVERT: B 47 TYR cc_start: 0.5947 (m-80) cc_final: 0.4828 (m-80) REVERT: B 177 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7165 (mtt-85) REVERT: B 189 ASP cc_start: 0.8760 (m-30) cc_final: 0.7869 (p0) REVERT: B 248 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7680 (mm-30) REVERT: C 189 ASP cc_start: 0.8908 (m-30) cc_final: 0.8079 (p0) REVERT: C 229 TYR cc_start: 0.8305 (p90) cc_final: 0.7944 (p90) REVERT: C 240 ILE cc_start: 0.8620 (mm) cc_final: 0.8420 (mm) REVERT: C 248 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8128 (mm-30) REVERT: C 359 TRP cc_start: 0.8377 (t60) cc_final: 0.8122 (t-100) REVERT: C 379 ASN cc_start: 0.7952 (t0) cc_final: 0.7618 (t0) REVERT: C 382 GLU cc_start: 0.7927 (tp30) cc_final: 0.7681 (tp30) REVERT: C 408 MET cc_start: 0.7947 (mtt) cc_final: 0.7573 (mtt) REVERT: D 80 GLU cc_start: 0.6858 (tt0) cc_final: 0.6492 (mt-10) REVERT: D 168 MET cc_start: 0.7967 (ttm) cc_final: 0.7654 (ttm) REVERT: D 189 ASP cc_start: 0.8358 (m-30) cc_final: 0.7959 (p0) REVERT: D 360 GLN cc_start: 0.7614 (tt0) cc_final: 0.7376 (tt0) REVERT: D 379 ASN cc_start: 0.7632 (t0) cc_final: 0.7342 (t0) REVERT: E 47 TYR cc_start: 0.4923 (m-80) cc_final: 0.3694 (m-80) REVERT: E 92 SER cc_start: 0.8313 (m) cc_final: 0.7966 (t) REVERT: E 94 LYS cc_start: 0.8415 (tttp) cc_final: 0.8098 (tttt) REVERT: E 116 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7125 (mt-10) REVERT: E 177 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7242 (mmt90) REVERT: E 189 ASP cc_start: 0.8485 (m-30) cc_final: 0.7450 (p0) REVERT: E 223 ARG cc_start: 0.7715 (ttm170) cc_final: 0.7344 (mtm180) REVERT: E 401 MET cc_start: 0.7584 (ttt) cc_final: 0.7267 (ttt) REVERT: F 80 GLU cc_start: 0.7601 (tt0) cc_final: 0.7214 (mt-10) REVERT: F 108 TYR cc_start: 0.7830 (t80) cc_final: 0.7176 (t80) REVERT: F 125 ASP cc_start: 0.5824 (m-30) cc_final: 0.5581 (p0) REVERT: F 134 SER cc_start: 0.8503 (m) cc_final: 0.8067 (p) REVERT: F 177 ARG cc_start: 0.7770 (mmm-85) cc_final: 0.7251 (mtt-85) REVERT: F 189 ASP cc_start: 0.8605 (m-30) cc_final: 0.7897 (p0) REVERT: F 234 CYS cc_start: 0.7455 (t) cc_final: 0.7122 (t) REVERT: F 390 GLU cc_start: 0.8197 (pm20) cc_final: 0.7731 (pm20) REVERT: G 47 TYR cc_start: 0.6153 (m-80) cc_final: 0.5183 (m-80) REVERT: G 177 ARG cc_start: 0.7831 (mmm-85) cc_final: 0.7596 (mmm-85) REVERT: G 189 ASP cc_start: 0.8821 (m-30) cc_final: 0.8112 (p0) REVERT: G 218 ARG cc_start: 0.8233 (mmt90) cc_final: 0.8022 (mtt90) outliers start: 24 outliers final: 20 residues processed: 443 average time/residue: 0.4069 time to fit residues: 259.1498 Evaluate side-chains 441 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 421 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain F residue 31 MET Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 210 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 141 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.134540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101070 restraints weight = 94292.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106002 restraints weight = 43633.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109321 restraints weight = 26010.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111492 restraints weight = 18311.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112870 restraints weight = 14486.612| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21210 Z= 0.121 Angle : 0.503 6.911 28763 Z= 0.266 Chirality : 0.038 0.167 3122 Planarity : 0.005 0.062 3696 Dihedral : 4.601 22.155 2870 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.99 % Allowed : 17.59 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.18), residues: 2541 helix: 1.03 (0.18), residues: 959 sheet: -0.95 (0.22), residues: 560 loop : -2.32 (0.22), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 223 TYR 0.015 0.001 TYR G 83 PHE 0.015 0.001 PHE F 179 TRP 0.010 0.001 TRP E 132 HIS 0.009 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00277 (21210) covalent geometry : angle 0.50320 (28763) hydrogen bonds : bond 0.02762 ( 768) hydrogen bonds : angle 3.96342 ( 2178) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 434 time to evaluate : 1.042 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 SER cc_start: 0.9180 (m) cc_final: 0.8477 (t) REVERT: A 116 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6545 (mp0) REVERT: A 186 ARG cc_start: 0.8528 (mtt180) cc_final: 0.8212 (ptp90) REVERT: A 189 ASP cc_start: 0.8385 (m-30) cc_final: 0.7850 (p0) REVERT: A 220 ILE cc_start: 0.9063 (mm) cc_final: 0.8842 (mm) REVERT: A 379 ASN cc_start: 0.7895 (t0) cc_final: 0.7580 (t0) REVERT: B 47 TYR cc_start: 0.6147 (m-80) cc_final: 0.4890 (m-80) REVERT: B 177 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7127 (mtt-85) REVERT: B 189 ASP cc_start: 0.8782 (m-30) cc_final: 0.7914 (p0) REVERT: B 248 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7729 (mm-30) REVERT: C 116 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7394 (mp0) REVERT: C 145 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7717 (mmmt) REVERT: C 189 ASP cc_start: 0.8964 (m-30) cc_final: 0.8096 (p0) REVERT: C 229 TYR cc_start: 0.8339 (p90) cc_final: 0.7987 (p90) REVERT: C 248 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8152 (mm-30) REVERT: C 359 TRP cc_start: 0.8337 (t60) cc_final: 0.8097 (t-100) REVERT: C 379 ASN cc_start: 0.8062 (t0) cc_final: 0.7721 (t0) REVERT: C 382 GLU cc_start: 0.8029 (tp30) cc_final: 0.7783 (tp30) REVERT: C 408 MET cc_start: 0.7644 (mtt) cc_final: 0.7252 (mtt) REVERT: D 168 MET cc_start: 0.7948 (ttm) cc_final: 0.7653 (ttm) REVERT: D 189 ASP cc_start: 0.8526 (m-30) cc_final: 0.7992 (p0) REVERT: D 379 ASN cc_start: 0.7734 (t0) cc_final: 0.7440 (t0) REVERT: D 401 MET cc_start: 0.7409 (tpt) cc_final: 0.6768 (tpp) REVERT: E 47 TYR cc_start: 0.5281 (m-80) cc_final: 0.3993 (m-80) REVERT: E 92 SER cc_start: 0.8418 (m) cc_final: 0.8108 (t) REVERT: E 94 LYS cc_start: 0.8397 (tttp) cc_final: 0.8078 (tttt) REVERT: E 116 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7121 (mt-10) REVERT: E 142 THR cc_start: 0.9089 (p) cc_final: 0.8876 (t) REVERT: E 165 LYS cc_start: 0.8634 (mmtt) cc_final: 0.8243 (mmtp) REVERT: E 177 ARG cc_start: 0.7877 (mmm-85) cc_final: 0.7228 (mmt90) REVERT: E 189 ASP cc_start: 0.8623 (m-30) cc_final: 0.7472 (p0) REVERT: E 223 ARG cc_start: 0.7798 (ttm170) cc_final: 0.7410 (mtm180) REVERT: E 401 MET cc_start: 0.7464 (ttt) cc_final: 0.7251 (ttt) REVERT: F 80 GLU cc_start: 0.7665 (tt0) cc_final: 0.7231 (mt-10) REVERT: F 134 SER cc_start: 0.8478 (m) cc_final: 0.8046 (p) REVERT: F 177 ARG cc_start: 0.7786 (mmm-85) cc_final: 0.7219 (mtt-85) REVERT: F 189 ASP cc_start: 0.8625 (m-30) cc_final: 0.7827 (p0) REVERT: F 213 LYS cc_start: 0.8148 (tptp) cc_final: 0.7855 (tptp) REVERT: F 365 PHE cc_start: 0.7017 (t80) cc_final: 0.6600 (t80) REVERT: G 47 TYR cc_start: 0.6141 (m-80) cc_final: 0.5231 (m-80) REVERT: G 177 ARG cc_start: 0.7799 (mmm-85) cc_final: 0.7563 (mmm-85) REVERT: G 189 ASP cc_start: 0.8941 (m-30) cc_final: 0.8136 (p0) outliers start: 22 outliers final: 20 residues processed: 443 average time/residue: 0.4004 time to fit residues: 255.1506 Evaluate side-chains 446 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 426 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain F residue 31 MET Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 383 HIS Chi-restraints excluded: chain G residue 100 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 134 optimal weight: 4.9990 chunk 69 optimal weight: 0.0370 chunk 0 optimal weight: 20.0000 chunk 141 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 132 optimal weight: 0.2980 chunk 237 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 218 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN E 314 ASN F 413 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102697 restraints weight = 93834.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107742 restraints weight = 43432.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111112 restraints weight = 25856.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113332 restraints weight = 18185.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114757 restraints weight = 14370.987| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21210 Z= 0.086 Angle : 0.487 6.992 28763 Z= 0.254 Chirality : 0.037 0.166 3122 Planarity : 0.005 0.102 3696 Dihedral : 4.386 19.994 2870 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.72 % Allowed : 18.26 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 2541 helix: 1.37 (0.18), residues: 931 sheet: -0.76 (0.22), residues: 560 loop : -2.11 (0.22), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 223 TYR 0.014 0.001 TYR B 369 PHE 0.021 0.001 PHE F 208 TRP 0.008 0.001 TRP C 214 HIS 0.009 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00199 (21210) covalent geometry : angle 0.48722 (28763) hydrogen bonds : bond 0.02392 ( 768) hydrogen bonds : angle 3.74912 ( 2178) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 439 time to evaluate : 1.108 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 SER cc_start: 0.9234 (m) cc_final: 0.8550 (t) REVERT: A 186 ARG cc_start: 0.8534 (mtt180) cc_final: 0.8273 (ptp90) REVERT: A 189 ASP cc_start: 0.8324 (m-30) cc_final: 0.7870 (p0) REVERT: A 227 LEU cc_start: 0.9072 (tt) cc_final: 0.8774 (tp) REVERT: A 248 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 379 ASN cc_start: 0.7838 (t0) cc_final: 0.7524 (t0) REVERT: B 47 TYR cc_start: 0.6028 (m-80) cc_final: 0.4899 (m-80) REVERT: B 177 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7151 (mtt-85) REVERT: B 189 ASP cc_start: 0.8718 (m-30) cc_final: 0.7884 (p0) REVERT: B 248 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7693 (mm-30) REVERT: B 401 MET cc_start: 0.7921 (tpt) cc_final: 0.6972 (tpt) REVERT: C 116 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7478 (mp0) REVERT: C 189 ASP cc_start: 0.8948 (m-30) cc_final: 0.8055 (p0) REVERT: C 229 TYR cc_start: 0.8325 (p90) cc_final: 0.8003 (p90) REVERT: C 248 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8123 (mm-30) REVERT: C 359 TRP cc_start: 0.8332 (t60) cc_final: 0.8094 (t-100) REVERT: C 379 ASN cc_start: 0.8008 (t0) cc_final: 0.7660 (t0) REVERT: C 382 GLU cc_start: 0.7981 (tp30) cc_final: 0.7603 (tp30) REVERT: C 408 MET cc_start: 0.7827 (mtt) cc_final: 0.7449 (mtt) REVERT: D 168 MET cc_start: 0.7904 (ttm) cc_final: 0.7622 (ttm) REVERT: D 189 ASP cc_start: 0.8387 (m-30) cc_final: 0.7922 (p0) REVERT: D 360 GLN cc_start: 0.7592 (tt0) cc_final: 0.7348 (tt0) REVERT: D 379 ASN cc_start: 0.7671 (t0) cc_final: 0.7373 (t0) REVERT: D 401 MET cc_start: 0.7348 (tpt) cc_final: 0.6709 (tpp) REVERT: E 47 TYR cc_start: 0.5256 (m-80) cc_final: 0.4685 (m-80) REVERT: E 92 SER cc_start: 0.8312 (m) cc_final: 0.7997 (t) REVERT: E 116 GLU cc_start: 0.7265 (mt-10) cc_final: 0.7008 (mt-10) REVERT: E 142 THR cc_start: 0.9052 (p) cc_final: 0.8850 (t) REVERT: E 165 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8251 (mmtp) REVERT: E 177 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.7238 (mmt90) REVERT: E 189 ASP cc_start: 0.8472 (m-30) cc_final: 0.7374 (p0) REVERT: E 223 ARG cc_start: 0.7744 (ttm170) cc_final: 0.7400 (mtm180) REVERT: E 401 MET cc_start: 0.8022 (ttt) cc_final: 0.7665 (ttt) REVERT: F 80 GLU cc_start: 0.7593 (tt0) cc_final: 0.7211 (mt-10) REVERT: F 134 SER cc_start: 0.8336 (m) cc_final: 0.7931 (p) REVERT: F 162 GLU cc_start: 0.7560 (tp30) cc_final: 0.7222 (tp30) REVERT: F 177 ARG cc_start: 0.7775 (mmm-85) cc_final: 0.7240 (mtt-85) REVERT: F 189 ASP cc_start: 0.8273 (m-30) cc_final: 0.7749 (p0) REVERT: F 234 CYS cc_start: 0.7514 (t) cc_final: 0.7112 (t) REVERT: F 365 PHE cc_start: 0.6967 (t80) cc_final: 0.6664 (t80) REVERT: F 390 GLU cc_start: 0.8214 (pm20) cc_final: 0.7788 (pm20) REVERT: G 47 TYR cc_start: 0.6115 (m-80) cc_final: 0.5218 (m-80) REVERT: G 98 ILE cc_start: 0.8949 (mm) cc_final: 0.8587 (mt) REVERT: G 133 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7743 (mm-30) REVERT: G 177 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7576 (mmm-85) REVERT: G 189 ASP cc_start: 0.8913 (m-30) cc_final: 0.8418 (p0) outliers start: 16 outliers final: 14 residues processed: 448 average time/residue: 0.3883 time to fit residues: 250.8570 Evaluate side-chains 442 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 428 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain F residue 31 MET Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 383 HIS Chi-restraints excluded: chain G residue 100 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 179 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 217 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN G 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.135435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101748 restraints weight = 94228.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106773 restraints weight = 43604.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110124 restraints weight = 25968.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112323 restraints weight = 18274.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.113697 restraints weight = 14451.550| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21210 Z= 0.113 Angle : 0.494 7.317 28763 Z= 0.260 Chirality : 0.037 0.164 3122 Planarity : 0.005 0.084 3696 Dihedral : 4.364 20.313 2870 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.72 % Allowed : 18.49 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.18), residues: 2541 helix: 1.38 (0.18), residues: 931 sheet: -0.73 (0.22), residues: 560 loop : -2.05 (0.22), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 56 TYR 0.012 0.001 TYR G 83 PHE 0.022 0.001 PHE F 208 TRP 0.009 0.001 TRP E 132 HIS 0.009 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00265 (21210) covalent geometry : angle 0.49357 (28763) hydrogen bonds : bond 0.02562 ( 768) hydrogen bonds : angle 3.76383 ( 2178) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 437 time to evaluate : 1.055 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 SER cc_start: 0.9234 (m) cc_final: 0.8533 (t) REVERT: A 186 ARG cc_start: 0.8558 (mtt180) cc_final: 0.8251 (ptp90) REVERT: A 189 ASP cc_start: 0.8272 (m-30) cc_final: 0.7875 (p0) REVERT: A 379 ASN cc_start: 0.7580 (t0) cc_final: 0.7227 (t0) REVERT: B 47 TYR cc_start: 0.6176 (m-80) cc_final: 0.4922 (m-80) REVERT: B 177 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7097 (mtt-85) REVERT: B 189 ASP cc_start: 0.8326 (m-30) cc_final: 0.7754 (p0) REVERT: B 248 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 323 GLU cc_start: 0.7981 (pm20) cc_final: 0.7777 (pm20) REVERT: C 116 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7548 (mp0) REVERT: C 189 ASP cc_start: 0.8827 (m-30) cc_final: 0.8071 (p0) REVERT: C 229 TYR cc_start: 0.8370 (p90) cc_final: 0.7995 (p90) REVERT: C 248 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8090 (mm-30) REVERT: C 359 TRP cc_start: 0.8375 (t60) cc_final: 0.8141 (t-100) REVERT: C 379 ASN cc_start: 0.7958 (t0) cc_final: 0.7598 (t0) REVERT: C 408 MET cc_start: 0.7805 (mtt) cc_final: 0.7418 (mtt) REVERT: D 168 MET cc_start: 0.7930 (ttm) cc_final: 0.7677 (ttm) REVERT: D 189 ASP cc_start: 0.8304 (m-30) cc_final: 0.7849 (p0) REVERT: D 360 GLN cc_start: 0.7629 (tt0) cc_final: 0.7400 (tt0) REVERT: D 379 ASN cc_start: 0.7629 (t0) cc_final: 0.7314 (t0) REVERT: D 401 MET cc_start: 0.7406 (tpt) cc_final: 0.6922 (tpp) REVERT: D 404 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7869 (mmtt) REVERT: E 47 TYR cc_start: 0.5365 (m-80) cc_final: 0.4734 (m-80) REVERT: E 92 SER cc_start: 0.8305 (m) cc_final: 0.8028 (t) REVERT: E 94 LYS cc_start: 0.8395 (tttp) cc_final: 0.8147 (tttt) REVERT: E 116 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6997 (mt-10) REVERT: E 165 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8267 (mmtp) REVERT: E 177 ARG cc_start: 0.7902 (mmm-85) cc_final: 0.7281 (mmt90) REVERT: E 189 ASP cc_start: 0.8377 (m-30) cc_final: 0.7362 (p0) REVERT: E 213 LYS cc_start: 0.8551 (tptp) cc_final: 0.8151 (tptp) REVERT: E 223 ARG cc_start: 0.7794 (ttm170) cc_final: 0.7480 (mtm180) REVERT: F 80 GLU cc_start: 0.7567 (tt0) cc_final: 0.7225 (mt-10) REVERT: F 134 SER cc_start: 0.8563 (m) cc_final: 0.8272 (p) REVERT: F 177 ARG cc_start: 0.7720 (mmm-85) cc_final: 0.7206 (mtt-85) REVERT: F 189 ASP cc_start: 0.8233 (m-30) cc_final: 0.7859 (p0) REVERT: F 234 CYS cc_start: 0.7453 (t) cc_final: 0.7087 (t) REVERT: F 365 PHE cc_start: 0.7089 (t80) cc_final: 0.6773 (t80) REVERT: F 390 GLU cc_start: 0.8248 (pm20) cc_final: 0.7806 (pm20) REVERT: G 47 TYR cc_start: 0.6180 (m-80) cc_final: 0.5315 (m-80) REVERT: G 133 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7835 (mm-30) REVERT: G 177 ARG cc_start: 0.7814 (mmm-85) cc_final: 0.7584 (mmm-85) REVERT: G 189 ASP cc_start: 0.8836 (m-30) cc_final: 0.8480 (p0) outliers start: 16 outliers final: 16 residues processed: 448 average time/residue: 0.3725 time to fit residues: 242.4489 Evaluate side-chains 442 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 426 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 383 HIS Chi-restraints excluded: chain G residue 100 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 158 optimal weight: 0.6980 chunk 217 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101876 restraints weight = 93907.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106912 restraints weight = 43532.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110284 restraints weight = 25909.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112469 restraints weight = 18255.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113904 restraints weight = 14465.063| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21210 Z= 0.109 Angle : 0.498 7.770 28763 Z= 0.261 Chirality : 0.037 0.165 3122 Planarity : 0.005 0.089 3696 Dihedral : 4.342 20.383 2870 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.95 % Allowed : 18.44 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.18), residues: 2541 helix: 1.44 (0.18), residues: 931 sheet: -0.68 (0.22), residues: 560 loop : -1.96 (0.22), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 223 TYR 0.017 0.001 TYR D 47 PHE 0.023 0.001 PHE F 208 TRP 0.009 0.001 TRP C 214 HIS 0.010 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00256 (21210) covalent geometry : angle 0.49834 (28763) hydrogen bonds : bond 0.02499 ( 768) hydrogen bonds : angle 3.72514 ( 2178) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 434 time to evaluate : 1.009 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 SER cc_start: 0.9231 (m) cc_final: 0.8521 (t) REVERT: A 186 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8253 (ptp90) REVERT: A 189 ASP cc_start: 0.8246 (m-30) cc_final: 0.7862 (p0) REVERT: A 366 GLN cc_start: 0.7655 (tp40) cc_final: 0.7435 (tp40) REVERT: A 379 ASN cc_start: 0.7565 (t0) cc_final: 0.7299 (t0) REVERT: B 47 TYR cc_start: 0.6214 (m-80) cc_final: 0.4933 (m-80) REVERT: B 177 ARG cc_start: 0.7747 (mmm-85) cc_final: 0.7099 (mtt-85) REVERT: B 189 ASP cc_start: 0.8323 (m-30) cc_final: 0.7754 (p0) REVERT: B 218 ARG cc_start: 0.7664 (mtt180) cc_final: 0.7408 (mtt180) REVERT: B 248 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 404 LYS cc_start: 0.7970 (mmtt) cc_final: 0.7556 (mmtt) REVERT: C 161 GLN cc_start: 0.7197 (mt0) cc_final: 0.6995 (mt0) REVERT: C 189 ASP cc_start: 0.8803 (m-30) cc_final: 0.8055 (p0) REVERT: C 229 TYR cc_start: 0.8367 (p90) cc_final: 0.7976 (p90) REVERT: C 240 ILE cc_start: 0.8771 (mm) cc_final: 0.8567 (mm) REVERT: C 248 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8077 (mm-30) REVERT: C 359 TRP cc_start: 0.8385 (t60) cc_final: 0.8155 (t-100) REVERT: C 379 ASN cc_start: 0.7963 (t0) cc_final: 0.7731 (t0) REVERT: C 382 GLU cc_start: 0.7724 (tp30) cc_final: 0.7443 (tp30) REVERT: C 408 MET cc_start: 0.7785 (mtt) cc_final: 0.7396 (mtt) REVERT: D 47 TYR cc_start: 0.7966 (t80) cc_final: 0.7735 (m-80) REVERT: D 168 MET cc_start: 0.7969 (ttm) cc_final: 0.7710 (ttm) REVERT: D 189 ASP cc_start: 0.8276 (m-30) cc_final: 0.7835 (p0) REVERT: D 360 GLN cc_start: 0.7613 (tt0) cc_final: 0.7375 (tt0) REVERT: D 379 ASN cc_start: 0.7613 (t0) cc_final: 0.7312 (t0) REVERT: D 401 MET cc_start: 0.7386 (tpt) cc_final: 0.6898 (tpp) REVERT: D 404 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7878 (mmtt) REVERT: E 47 TYR cc_start: 0.5458 (m-80) cc_final: 0.4750 (m-80) REVERT: E 92 SER cc_start: 0.8211 (m) cc_final: 0.7854 (t) REVERT: E 94 LYS cc_start: 0.8443 (tttp) cc_final: 0.8140 (tttt) REVERT: E 165 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8272 (mmtp) REVERT: E 177 ARG cc_start: 0.7911 (mmm-85) cc_final: 0.7285 (mmt90) REVERT: E 189 ASP cc_start: 0.8349 (m-30) cc_final: 0.7337 (p0) REVERT: E 213 LYS cc_start: 0.8512 (tptp) cc_final: 0.8082 (tptp) REVERT: E 223 ARG cc_start: 0.7782 (ttm170) cc_final: 0.7474 (mtm180) REVERT: F 80 GLU cc_start: 0.7548 (tt0) cc_final: 0.7231 (mt-10) REVERT: F 134 SER cc_start: 0.8551 (m) cc_final: 0.8280 (p) REVERT: F 177 ARG cc_start: 0.7729 (mmm-85) cc_final: 0.7216 (mtt-85) REVERT: F 189 ASP cc_start: 0.8212 (m-30) cc_final: 0.7814 (p0) REVERT: F 234 CYS cc_start: 0.7426 (t) cc_final: 0.7059 (t) REVERT: F 365 PHE cc_start: 0.7076 (t80) cc_final: 0.6761 (t80) REVERT: F 390 GLU cc_start: 0.8245 (pm20) cc_final: 0.7810 (pm20) REVERT: G 47 TYR cc_start: 0.6191 (m-80) cc_final: 0.5314 (m-80) REVERT: G 133 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7855 (mm-30) REVERT: G 177 ARG cc_start: 0.7814 (mmm-85) cc_final: 0.7585 (mmm-85) REVERT: G 189 ASP cc_start: 0.8803 (m-30) cc_final: 0.8459 (p0) REVERT: G 383 HIS cc_start: 0.7430 (m90) cc_final: 0.6872 (m90) outliers start: 21 outliers final: 18 residues processed: 450 average time/residue: 0.3812 time to fit residues: 249.2676 Evaluate side-chains 449 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 431 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 399 TYR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 383 HIS Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain G residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 23 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 173 optimal weight: 0.2980 chunk 178 optimal weight: 0.0040 chunk 31 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 222 optimal weight: 0.7980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN B 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.135732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101835 restraints weight = 93629.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106886 restraints weight = 43629.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110247 restraints weight = 26061.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112477 restraints weight = 18400.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113911 restraints weight = 14545.142| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21210 Z= 0.107 Angle : 0.498 8.326 28763 Z= 0.260 Chirality : 0.037 0.165 3122 Planarity : 0.005 0.105 3696 Dihedral : 4.313 20.478 2870 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.99 % Allowed : 18.63 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.18), residues: 2541 helix: 1.48 (0.18), residues: 931 sheet: -0.63 (0.22), residues: 560 loop : -1.91 (0.22), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 223 TYR 0.012 0.001 TYR D 47 PHE 0.024 0.001 PHE F 208 TRP 0.008 0.001 TRP E 132 HIS 0.009 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00251 (21210) covalent geometry : angle 0.49770 (28763) hydrogen bonds : bond 0.02450 ( 768) hydrogen bonds : angle 3.68960 ( 2178) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 434 time to evaluate : 0.947 Fit side-chains TARDY: cannot create tardy model for: "MET A 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 48 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7926 (mmm160) cc_final: 0.7529 (mmt180) REVERT: A 92 SER cc_start: 0.9237 (m) cc_final: 0.8535 (t) REVERT: A 116 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6392 (mp0) REVERT: A 186 ARG cc_start: 0.8543 (mtt180) cc_final: 0.8252 (ptp90) REVERT: A 189 ASP cc_start: 0.8310 (m-30) cc_final: 0.7852 (p0) REVERT: A 223 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7836 (ttp-110) REVERT: A 366 GLN cc_start: 0.7854 (tp40) cc_final: 0.7469 (tp-100) REVERT: A 379 ASN cc_start: 0.7500 (t0) cc_final: 0.7114 (t0) REVERT: B 47 TYR cc_start: 0.6102 (m-80) cc_final: 0.4678 (m-80) REVERT: B 73 ARG cc_start: 0.7892 (tpt170) cc_final: 0.7569 (tpt170) REVERT: B 98 ILE cc_start: 0.8530 (mm) cc_final: 0.8128 (mt) REVERT: B 177 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.7090 (mtt-85) REVERT: B 189 ASP cc_start: 0.8327 (m-30) cc_final: 0.7754 (p0) REVERT: B 248 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7764 (mm-30) REVERT: C 161 GLN cc_start: 0.7295 (mt0) cc_final: 0.7044 (mt0) REVERT: C 189 ASP cc_start: 0.8810 (m-30) cc_final: 0.8111 (p0) REVERT: C 213 LYS cc_start: 0.7915 (tmtt) cc_final: 0.7467 (tptp) REVERT: C 229 TYR cc_start: 0.8362 (p90) cc_final: 0.8033 (p90) REVERT: C 240 ILE cc_start: 0.8765 (mm) cc_final: 0.8564 (mm) REVERT: C 248 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8083 (mm-30) REVERT: C 359 TRP cc_start: 0.8381 (t60) cc_final: 0.8151 (t-100) REVERT: C 379 ASN cc_start: 0.7973 (t0) cc_final: 0.7739 (t0) REVERT: C 408 MET cc_start: 0.7767 (mtt) cc_final: 0.7378 (mtt) REVERT: D 47 TYR cc_start: 0.7951 (t80) cc_final: 0.7748 (m-80) REVERT: D 168 MET cc_start: 0.7970 (ttm) cc_final: 0.7711 (ttm) REVERT: D 189 ASP cc_start: 0.8277 (m-30) cc_final: 0.7835 (p0) REVERT: D 360 GLN cc_start: 0.7601 (tt0) cc_final: 0.7354 (tt0) REVERT: D 379 ASN cc_start: 0.7631 (t0) cc_final: 0.7325 (t0) REVERT: D 401 MET cc_start: 0.7359 (tpt) cc_final: 0.6880 (tpp) REVERT: D 404 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7895 (mmtt) REVERT: E 47 TYR cc_start: 0.5494 (m-80) cc_final: 0.4753 (m-80) REVERT: E 92 SER cc_start: 0.8298 (m) cc_final: 0.7985 (t) REVERT: E 94 LYS cc_start: 0.8557 (tttp) cc_final: 0.8182 (tttt) REVERT: E 165 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8273 (mmtp) REVERT: E 177 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7288 (mmt90) REVERT: E 189 ASP cc_start: 0.8347 (m-30) cc_final: 0.7334 (p0) REVERT: E 213 LYS cc_start: 0.8523 (tptp) cc_final: 0.8095 (tptp) REVERT: F 31 MET cc_start: 0.0539 (mpp) cc_final: 0.0005 (tpt) REVERT: F 80 GLU cc_start: 0.7536 (tt0) cc_final: 0.7234 (mt-10) REVERT: F 134 SER cc_start: 0.8558 (m) cc_final: 0.8281 (p) REVERT: F 177 ARG cc_start: 0.7735 (mmm-85) cc_final: 0.7217 (mtt-85) REVERT: F 189 ASP cc_start: 0.8216 (m-30) cc_final: 0.7805 (p0) REVERT: F 234 CYS cc_start: 0.7419 (t) cc_final: 0.7062 (t) REVERT: F 365 PHE cc_start: 0.7062 (t80) cc_final: 0.6736 (t80) REVERT: F 390 GLU cc_start: 0.8243 (pm20) cc_final: 0.7811 (pm20) REVERT: G 47 TYR cc_start: 0.6196 (m-80) cc_final: 0.5329 (m-80) REVERT: G 133 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7870 (mm-30) REVERT: G 177 ARG cc_start: 0.7816 (mmm-85) cc_final: 0.7580 (mmm-85) REVERT: G 189 ASP cc_start: 0.8766 (m-30) cc_final: 0.8398 (p0) REVERT: G 383 HIS cc_start: 0.7420 (m90) cc_final: 0.6858 (m90) outliers start: 22 outliers final: 22 residues processed: 450 average time/residue: 0.3897 time to fit residues: 253.8177 Evaluate side-chains 447 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 425 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 399 TYR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 383 HIS Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 134 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 180 optimal weight: 30.0000 chunk 150 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 219 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 213 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 HIS B 314 ASN B 332 ASN C 332 ASN E 127 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.134967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101118 restraints weight = 94595.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106113 restraints weight = 44107.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109455 restraints weight = 26390.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111653 restraints weight = 18650.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113058 restraints weight = 14775.916| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 21210 Z= 0.196 Angle : 0.677 59.199 28763 Z= 0.386 Chirality : 0.039 0.173 3122 Planarity : 0.005 0.104 3696 Dihedral : 4.313 19.879 2870 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 1.13 % Allowed : 18.81 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 2541 helix: 1.45 (0.18), residues: 931 sheet: -0.64 (0.22), residues: 560 loop : -1.92 (0.22), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 223 TYR 0.014 0.001 TYR A 60 PHE 0.023 0.002 PHE F 208 TRP 0.010 0.001 TRP E 132 HIS 0.009 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00433 (21210) covalent geometry : angle 0.67697 (28763) hydrogen bonds : bond 0.02581 ( 768) hydrogen bonds : angle 3.73773 ( 2178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7034.48 seconds wall clock time: 120 minutes 20.61 seconds (7220.61 seconds total)